RetrogeneDB ID: | retro_btau_353 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 10:76383218..76383497(+) | ||
| Located in intron of: | ENSBTAG00000025450 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NIP7 | ||
| Ensembl ID: | ENSBTAG00000001666 | ||
| Aliases: | None | ||
| Description: | 60S ribosome subunit biogenesis protein NIP7 homolog [Source:RefSeq peptide;Acc:NP_001179168] |
Retrocopy-Parental alignment summary:
>retro_btau_353
CCTCTGACTGAAGAGGAGACCCATGTAATGTTTGAGAAGACAGCAAAATTCGTCAGAGAGAACCTTCAGCTGCTGGTCAA
CAGGTCCTATGGCACCCATGGTTTCAGGCGGCACAATGACTGGACAGTGTACTATGTGAATGAGATGATCTTGAAGTTGG
TTGTGGGTATCTCTGGTGACAAGCTGGTTTTGCTTGGGAGGTACTTTGGAAAATTCCCTAAGACCCACAAGTTTCAGTTG
GACATATCAGCTCTGGATTACCTTGCACCCTATGCCAAG
ORF - retro_btau_353 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.12 % |
| Parental protein coverage: | 51.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHND-RVYYVSEKILKLAANISGDKLVSLGTCFG |
| PLTEEET.VMFEK.AK...ENLQLLV.R..GT..FR.HND..VYYV.E.ILKL...ISGDKLV.LG..FG | |
| Retrocopy | PLTEEETHVMFEKTAKFVRENLQLLVNRSYGTHGFRRHNDWTVYYVNEMILKLVVGISGDKLVLLGRYFG |
| Parental | KFTKTHKFRLHITALDYLAPYAK |
| KF.KTHKF.L.I.ALDYLAPYAK | |
| Retrocopy | KFPKTHKFQLDISALDYLAPYAK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| ERP005899_liver | 0 .07 RPM | 2 .45 RPM |
| ERP005899_muscle | 0 .00 RPM | 4 .43 RPM |
| SRP017611_brain | 0 .00 RPM | 7 .45 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .77 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .04 RPM |
| SRP030211_testis | 0 .01 RPM | 10 .00 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_353 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_353 was not experimentally validated.